1. Automated generation of large phylogenies
and a probabilistically time-scaled 1,000-taxon
phylogenetic hypothesis for Mesozoic
dinosaurs: dating the origins of flight and
crown-birds
Graeme T. Lloyd David W. Bapst
@GraemeTLloyd @dwbapst
Katie E. Davis Matt Friedman
@drkatiedavis @Friedman_Lab

2. When?
1. Dinosaurs
2. Flight
3. Crown birds

3. Simultaneous inference
Lee et al 2014

4. A posteriori time-scaling
paleotree
strap

5. A posteriori time-scaling
+
paleotree
strap

6. A posteriori time-scaling
+ =
paleotree
strap

7. A posteriori time-scaling
Arbitrary
Branch-sharing
Ruta et al 2006; Brusatte et al 2008
Arbitrary addition(s)
Derstler 1982
Minimum branch-length
Laurin 2004

8. A posteriori time-scaling
cal3
Bapst 2013
Hedman method
Lloyd and Friedman in prep
Nowak
Nowak et al 2013
Arbitrary Probabilistic
Branch-sharing
Ruta et al 2006; Brusatte et al 2008
Arbitrary addition(s)
Derstler 1982
Minimum branch-length
Laurin 2004

9. A posteriori time-scaling
cal3
Bapst 2013
Hedman method
Lloyd and Friedman in prep
Arbitrary Probabilistic

10. cal3 method
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Bapst 2013

11. cal3 method
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Bapst 2013

12. cal3 method
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Bapst 2013

13. cal3 method
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Bapst 2013

14. Hedman method
Target node Outgroup taxon
TIME
Hedman 2010; Lloyd and Friedman in prep

15. Hedman method
Target node Outgroup taxon
TIME
Hedman 2010; Lloyd and Friedman in prep

16. Lloyd et al. 2008Pisani et al. 2002
Phylogenetic approach

17. Pipeline
Collect
data
graemetlloyd.com

18. Pipeline
Collect
data
Reconcile
taxonomy

19. Pipeline
Collect
data
Reconcile
taxonomy
Define
cutoff

20. Pipeline
Collect
data
Reconcile
taxonomy
Define
cutoff
Consensus
vs. MPTs

21. Taxonomy
tree
Pipeline
A
B
C
D
E
F
G
H
I
J
K
L
Class Order Family Genus

22. Taxonomy
tree
Safe Taxon.
Reduction
Pipeline
github.com/graemetlloyd/Claddis
Wilkinson 1995

23. Taxonomy
tree
Safe Taxon.
Reduction
Weights
Pipeline

24. Taxonomy
tree
Safe Taxon.
Reduction
Weights Inference
Pipeline

25. Taxonomy
tree
Safe Taxon.
Reduction
Weights Inference
Pipeline

26. Results
cal3Hedman

27. Dinosauria
cal3Hedman

28. Dinosauria
2.6%
9.6%
cal3Hedman

29. Dinosauria
0.2%
1.0%
cal3Hedman
-

30. Aves
cal3Hedman

31. Aves
cal3Hedman

32. Crown birds
cal3Hedman

33. Crown birds
cal3
Hedman
95% HPD

34. Crown birds
cal3
Molecular Clock
Hedman
95% HPD

35. Crown birds
cal3
Molecular Clock
Hedman
Morphological Clock
95% HPD

36. Conclusions
Hedman
cal3

37. Conclusions
Hedman
cal3

38. Conclusions
Hedman
cal3

39. Conclusions
Hedman
cal3